The purpose of this model is to understand how genetic architectures of alternative reproductive tactics impact their maintenance in populations. I’m using an individual-based simulation model with different selection scenarios, types of alternative tactics, and genetic architectures (genome-wide additive genetic variance, supergenes, expression networks).

Overview of the model

Males can be courters or not-courters and parents or not-parents. When the model is run with both traits, this results in four possible morphs: courter/parent, courter/not-parent, not-courter/parent, and not-courter/not-parent. Generations are non-overlapping and there is one reproductive bout per generation. In each generation, the population follows the following timeline:

Fig. 1 Flowchart of simulation

Fig. 1 Flowchart of simulation

each step is explained in further detail below.

1. Choosing a nest

A female samples 50 males and chooses a male to nest with based on his courtship trait. If there are no courtship traits in the model, she chooses based on the male’s parental trait. If she does not encouter an acceptable male, she does not nest. If she encounters multiple equally-acceptable males, she randomly selects one of them.

2. Fertilization

Once a female decides to nest, up to three males can fertilize the nest. Courters and parental males can contribute more sperm than non-courter and non-parental males: \(r_{courter}=r_{parent}=8\) and \(r_{non-courter}=r_{non-parent}=4\). A courter/non-parent has \(r_{non-parent}\) and a non-courter/parent has \(r_{parent}\). The male with whom the female is nesting gets \(r_{parent}/\Sigma{n_{sperm}}\) and additional non-parental males (up to 2) get \((r_{non-parent}*0.5/\Sigma{n_{sperm}})\), where \(\Sigma{n_{sperm}}\) is the total number of sperm contributed by all of the males, weighted by the sperm competition factor (0.5 is the default for all males except the nesting male). So, when a female mates with one courter and two non-parentals, \(\Sigma{n_{sperm}}\) = \(r_{courter}\) + 2\(*\)(0.5\(*\)\(r_{sneaker}\)), where \(r_{courter}\) = 8 and \(r_{sneaker}\) = 4, therefore \(\Sigma{n_{sperm}}\) = 12.

That being said, every time a male mates he uses his sperm, so after one mating where a courter fertilizes 50% of the female’s 4 eggs, he only has 6 sperm for his next mating.

3. Nest Survival

Before the babies can survive, the nest has to survive. This step is only relevant when parental traits are in the model - if only the courtship trait is specified, then all progeny in the nest survive at this point. When males have the parental trait, if the female has given eggs to a non-parental male (because she chose based on courtship traits), then the nest has a 10% chance of surviving. If the female has given eggs to a parental male, the nest has a 90% chance of surviving.

4. Density-dependent survival

Once the identities of the surviving nests are known–along with the identities of the parents, including sneaker parents–the offspring are created in the simulation. The offspring are created to fill the full carrying capacity of the population, with the numbers per nest being equally divided among all surviving offspring. This allows the population to maintain a constant population size (prior to viability selection) while maintaining the relative successes of the given genotypes/morphs.

5. Viability selection

Before becoming adults, the offspring experience viability selection. Courters and parental males are disfavored in viability selection, with a survival probability of 0.9950125. If an individual is both a courter and a parental male, the survival probability is 0.9900498. Non-courters and non-parental males have survival probabilities of 1.

Evaluating equilibrium

After 10000 generations, I begin tracking the change in frequency of the courter and parent traits, and do so for 2000 additional generations. I calculate the variance in the change in frequency over those 2000 generations. I declare an equilibrium (‘stasis’) has been reached if the last change in frequency of both traits is less than the variance in changes in frequency.

Unlinked additive genetic variance

In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles are all freely recombining and are not adhered to any physical genomic location (aka this is a classical quantitative genetics approach). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

Females choose nests based on whether the male is a courter or not, and they all prefer courters all of the time (the female preference does not have a genetic basis and does not evolve). The only way that non-courters produce offspring is through sneaking, but all males can be sneakers (both courters and non-courters). Because parental care is not incorporated in this model, all nests survive.

With viability selection

Frequency of the courter morph with unlinked additive genetic variances in all of the replicates

Frequency of the courter morph with unlinked additive genetic variances in all of the replicates

Of the 20 replicates, 20 reached a steady state by 10000 generations. The different runs all overlap, suggesting that they all converge on the same outcome: all males are courters. This result is also obvious by inspecting a table of courter frequencies and fitnesses in the final generation of the runs.

In some cases, major differences emerge between scenarios with viability selection and without, so below I present each case with and without viability selection

Frequency of courters in final generation of runs with unlinked additive genetic variances
CourterFreq CourterW NonCourterW
courter_unlinked_1_summary.txt_1 1 2.07708 0
courter_unlinked_1_summary.txt_2 1 2.04330 0
courter_unlinked_1_summary.txt_3 1 1.99799 0
courter_unlinked_1_summary.txt_4 1 2.00605 0
courter_unlinked_2_summary.txt_1 1 2.07708 0
courter_unlinked_2_summary.txt_2 1 2.04330 0
courter_unlinked_2_summary.txt_3 1 1.99799 0
courter_unlinked_2_summary.txt_4 1 2.00605 0
courter_unlinked_3_summary.txt_1 1 1.90267 0
courter_unlinked_3_summary.txt_2 1 2.00604 0
courter_unlinked_3_summary.txt_3 1 1.93933 0
courter_unlinked_3_summary.txt_4 1 1.99198 0
courter_unlinked_4_summary.txt_1 1 2.02020 0
courter_unlinked_4_summary.txt_2 1 1.97628 0
courter_unlinked_4_summary.txt_3 1 1.87970 0
courter_unlinked_4_summary.txt_4 1 1.93798 0
courter_unlinked_5_summary.txt_1 1 2.02020 0
courter_unlinked_5_summary.txt_2 1 1.97628 0
courter_unlinked_5_summary.txt_3 1 1.87970 0
courter_unlinked_5_summary.txt_4 1 1.93798 0

We may also be interested in the evolution of the courter trait values, which reflects the additive effects of all loci.

Evolution of courtship trait with unlinked loci. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of courtship trait with unlinked loci. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Without viability selection

Frequency of the courter morph with unlinked additive genetic variances and without viability selection in all of the replicates

Frequency of the courter morph with unlinked additive genetic variances and without viability selection in all of the replicates

Of the 20 replicates, 20 reached a steady state by 10000 generations. The different runs all overlap, suggesting that they all converge on the same outcome: all males are courters. This result is also obvious by inspecting a table of courter frequencies and fitnesses in the final generation of the runs.

Frequency of courters in final generation of runs with unlinked additive genetic variances and no viability selection
CourterFreq CourterW NonCourterW
courter_unlinked_novs_1_summary.txt_1 1 1.90476 0
courter_unlinked_novs_1_summary.txt_2 1 1.94932 0
courter_unlinked_novs_1_summary.txt_3 1 2.13675 0
courter_unlinked_novs_1_summary.txt_4 1 1.97239 0
courter_unlinked_novs_2_summary.txt_1 1 1.90476 0
courter_unlinked_novs_2_summary.txt_2 1 1.94932 0
courter_unlinked_novs_2_summary.txt_3 1 2.13675 0
courter_unlinked_novs_2_summary.txt_4 1 1.97239 0
courter_unlinked_novs_3_summary.txt_1 1 2.01207 0
courter_unlinked_novs_3_summary.txt_2 1 2.02840 0
courter_unlinked_novs_3_summary.txt_3 1 1.99203 0
courter_unlinked_novs_3_summary.txt_4 1 1.97628 0
courter_unlinked_novs_4_summary.txt_1 1 1.91571 0
courter_unlinked_novs_4_summary.txt_2 1 1.91571 0
courter_unlinked_novs_4_summary.txt_3 1 1.94553 0
courter_unlinked_novs_4_summary.txt_4 1 1.95312 0
courter_unlinked_novs_5_summary.txt_1 1 2.02429 0
courter_unlinked_novs_5_summary.txt_2 1 2.13220 0
courter_unlinked_novs_5_summary.txt_3 1 1.94553 0
courter_unlinked_novs_5_summary.txt_4 1 2.00000 0

We may also be interested in the evolution of the courter trait values, which reflects the additive effects of all loci.

Evolution of courtship trait with unlinked loci and no viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of courtship trait with unlinked loci and no viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Parental trait

In this case, there are no courtship traits so females lay eggs in nests randomly. Non-parental males will sneak fertilizations in parental males’ nests. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

With viability selection

Frequency of parent morph with unlinked loci (each color represents a different replicate)

Frequency of parent morph with unlinked loci (each color represents a different replicate)

Again, inference is facilitated by looking at the final frequencies and fitnesses in each replicate:

Frequency of parents in final generation
ParentFreq ParentW NonParentW
parent_unlinked_1_summary.txt_1 0.875717 1.54803 0.569231
parent_unlinked_1_summary.txt_2 0.863281 1.64027 0.771429
parent_unlinked_1_summary.txt_3 0.873494 1.66207 0.746032
parent_unlinked_1_summary.txt_4 0.866534 1.71264 0.746269
parent_unlinked_2_summary.txt_1 0.875717 1.54803 0.569231
parent_unlinked_2_summary.txt_2 0.863281 1.64027 0.771429
parent_unlinked_2_summary.txt_3 0.873494 1.66207 0.746032
parent_unlinked_2_summary.txt_4 0.866534 1.71264 0.746269
parent_unlinked_3_summary.txt_1 0.545977 1.49474 0.291139
parent_unlinked_3_summary.txt_2 0.517625 1.31900 0.250000
parent_unlinked_3_summary.txt_3 0.568898 1.55017 0.315068
parent_unlinked_3_summary.txt_4 0.528736 1.50000 0.300813
parent_unlinked_4_summary.txt_1 0.907445 1.75388 1.021740
parent_unlinked_4_summary.txt_2 0.930769 1.60124 1.222220
parent_unlinked_4_summary.txt_3 0.908184 1.64396 0.869565
parent_unlinked_4_summary.txt_4 0.927856 1.72570 0.666667
parent_unlinked_5_summary.txt_1 0.501976 1.31496 0.269841
parent_unlinked_5_summary.txt_2 0.521042 1.33846 0.334728
parent_unlinked_5_summary.txt_3 0.570499 1.76046 0.333333
parent_unlinked_5_summary.txt_4 0.584071 1.54545 0.361702

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Let’s take a look at how the parent trait values evolve

Evolution of parenting trait values with additive genetic variation. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with additive genetic variation. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Without viability selection

Frequency of parent morph with unlinked loci without viability selection for all replicates

Frequency of parent morph with unlinked loci without viability selection for all replicates

Again, let’s look at the final frequencies and fitnesses in each replicate:

Frequency of parents in final generation
ParentFreq ParentW NonParentW
parent_unlinked_novs_1_summary.txt_1 0.889546 1.70067 0.928571
parent_unlinked_novs_1_summary.txt_2 0.895464 1.59031 1.169810
parent_unlinked_novs_1_summary.txt_3 0.885932 1.56009 0.816667
parent_unlinked_novs_1_summary.txt_4 0.907692 1.65678 0.916667
parent_unlinked_novs_2_summary.txt_1 0.889546 1.70067 0.928571
parent_unlinked_novs_2_summary.txt_2 0.895464 1.59031 1.169810
parent_unlinked_novs_2_summary.txt_3 0.885932 1.56009 0.816667
parent_unlinked_novs_2_summary.txt_4 0.907692 1.65678 0.916667
parent_unlinked_novs_3_summary.txt_1 0.875728 1.53659 0.812500
parent_unlinked_novs_3_summary.txt_2 0.886869 1.67426 0.982143
parent_unlinked_novs_3_summary.txt_3 0.853707 1.72770 0.684932
parent_unlinked_novs_3_summary.txt_4 0.873706 1.68246 0.934426
parent_unlinked_novs_4_summary.txt_1 0.933884 1.74779 1.250000
parent_unlinked_novs_4_summary.txt_2 0.910646 1.59708 0.744681
parent_unlinked_novs_4_summary.txt_3 0.922921 1.64615 1.184210
parent_unlinked_novs_4_summary.txt_4 0.911067 1.59436 0.800000
parent_unlinked_novs_5_summary.txt_1 0.578313 1.50000 0.219048
parent_unlinked_novs_5_summary.txt_2 0.553606 1.39437 0.497817
parent_unlinked_novs_5_summary.txt_3 0.575049 1.57288 0.311927
parent_unlinked_novs_5_summary.txt_4 0.538603 1.29352 0.250996

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Let’s take a look at how the parent trait values evolve

Evolution of parenting trait values with additive genetic variation and no viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with additive genetic variation and no viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters and non-parents can reproduce through sneaking.

With viability selection

The different runs have different outcomes.

Let’s look at the morph frequencies for each run.

Frequency of the 4 morphs in each rep with unlinked genetic variation

Frequency of the 4 morphs in each rep with unlinked genetic variation

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_unlinked_1_summary.txt_1 11999 Pop0 919 462 457 1000 0.4441960 0.924242 0.7394770 0.4972080 2.00703 1.428570 -0.5382970 0.924242 -0.399304 0.2340440 2.007030 1.42857 0.0757576 0.000000 0.000000 0.924242 NA NA
parent-courter_unlinked_1_summary.txt_2 11999 Pop1 933 458 475 1000 0.4441960 0.943231 0.7820730 0.5091930 1.94907 2.615380 -0.5382970 0.943231 -0.379253 0.2396850 1.949070 2.61538 0.0567686 0.000000 0.000000 0.943231 NA NA
parent-courter_unlinked_1_summary.txt_3 11999 Pop2 969 453 516 1000 0.4441960 0.922737 0.7033820 0.4746840 1.95455 1.971430 -0.5382970 0.922737 -0.416294 0.2234410 1.954550 1.97143 0.0772627 0.000000 0.000000 0.922737 NA NA
parent-courter_unlinked_1_summary.txt_4 11999 Pop3 944 493 451 1000 0.4441960 0.920892 0.7416680 0.5012960 1.83700 1.846150 -0.5382970 0.920892 -0.398273 0.2359680 1.837000 1.84615 0.0791075 0.000000 0.000000 0.920892 NA NA
parent-courter_unlinked_2_summary.txt_1 11999 Pop0 919 462 457 1000 0.4441960 0.924242 0.7394770 0.4972080 2.00703 1.428570 -0.5382970 0.924242 -0.399304 0.2340440 2.007030 1.42857 0.0757576 0.000000 0.000000 0.924242 NA NA
parent-courter_unlinked_2_summary.txt_2 11999 Pop1 933 458 475 1000 0.4441960 0.943231 0.7820730 0.5091930 1.94907 2.615380 -0.5382970 0.943231 -0.379253 0.2396850 1.949070 2.61538 0.0567686 0.000000 0.000000 0.943231 NA NA
parent-courter_unlinked_2_summary.txt_3 11999 Pop2 969 453 516 1000 0.4441960 0.922737 0.7033820 0.4746840 1.95455 1.971430 -0.5382970 0.922737 -0.416294 0.2234410 1.954550 1.97143 0.0772627 0.000000 0.000000 0.922737 NA NA
parent-courter_unlinked_2_summary.txt_4 11999 Pop3 944 493 451 1000 0.4441960 0.920892 0.7416680 0.5012960 1.83700 1.846150 -0.5382970 0.920892 -0.398273 0.2359680 1.837000 1.84615 0.0791075 0.000000 0.000000 0.920892 NA NA
parent-courter_unlinked_3_summary.txt_1 11999 Pop0 987 501 486 1000 0.3715940 0.399202 0.3103690 0.6270920 0.00000 0.312292 -0.3750940 0.600798 -0.356136 0.1941720 0.312292 0.00000 0.0000000 0.600798 0.399202 0.000000 NA NA
parent-courter_unlinked_3_summary.txt_2 11999 Pop1 984 488 496 1000 0.3715940 0.409836 0.3115760 0.6339380 0.00000 0.336806 -0.3750940 0.590164 -0.356510 0.1962910 0.336806 0.00000 0.0000000 0.590164 0.409836 0.000000 NA NA
parent-courter_unlinked_3_summary.txt_3 11999 Pop2 981 479 502 1000 0.3715940 0.421712 0.3049590 0.6456720 0.00000 0.382671 -0.3750940 0.578288 -0.354461 0.1999240 0.382671 0.00000 0.0000000 0.578288 0.421712 0.000000 NA NA
parent-courter_unlinked_3_summary.txt_4 11999 Pop3 983 485 498 1000 0.3715940 0.416495 0.3181010 0.6351320 0.00000 0.268551 -0.3750940 0.583505 -0.358530 0.1966610 0.268551 0.00000 0.0000000 0.583505 0.416495 0.000000 NA NA
parent-courter_unlinked_4_summary.txt_1 11999 Pop0 987 509 478 1000 0.0606641 0.919450 0.1638190 0.1735360 1.73718 1.536590 0.0498541 0.919450 0.204422 0.2600290 1.737180 1.53659 0.0805501 0.000000 0.000000 0.919450 NA NA
parent-courter_unlinked_4_summary.txt_2 11999 Pop1 989 514 475 1000 0.0606641 0.887160 0.1454410 0.1707650 1.83114 1.051720 0.0498541 0.887160 0.176885 0.2558760 1.831140 1.05172 0.1128400 0.000000 0.000000 0.887160 NA NA
parent-courter_unlinked_4_summary.txt_3 11999 Pop2 1000 505 495 1000 0.0606641 0.893069 0.1663580 0.1821390 1.80931 1.074070 0.0498541 0.893069 0.208227 0.2729190 1.809310 1.07407 0.1069310 0.000000 0.000000 0.893069 NA NA
parent-courter_unlinked_4_summary.txt_4 11999 Pop3 1000 526 474 1000 0.0606641 0.914449 0.1547000 0.1691010 1.73181 1.355560 0.0498541 0.914449 0.190759 0.2533830 1.731810 1.35556 0.0855513 0.000000 0.000000 0.914449 NA NA
parent-courter_unlinked_5_summary.txt_1 256 Pop0 4 3 1 4 -0.0371052 0.000000 -0.0632447 0.0261395 0.00000 1.333330 -0.5026820 1.000000 -0.468886 0.0337960 1.333330 0.00000 0.0000000 1.000000 0.000000 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_2 256 Pop1 27 18 9 29 -0.0371052 0.444444 -0.0514503 0.0194850 0.00000 0.000000 -0.5026820 0.555556 -0.484135 0.0251924 0.000000 0.00000 0.0000000 0.555556 0.444444 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_3 256 Pop2 36 20 16 52 -0.0371052 0.250000 -0.0566104 0.0226383 0.00000 0.533333 -0.5026820 0.750000 -0.477463 0.0292693 0.533333 0.00000 0.0000000 0.750000 0.250000 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_4 256 Pop3 304 163 141 295 -0.0371052 0.546012 -0.0415916 0.0224962 0.00000 0.324324 -0.5026820 0.453988 -0.496881 0.0290856 0.324324 0.00000 0.0000000 0.453988 0.546012 0.000000 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter.

If we look at how the two traits evolved, we see that in the runs when the population crashed the trait values did not immediately evolve above the thresholds (unlike in the other runs) – and that the parent threshold started out much lower than the courter threshold. It may be that the threshold value plays a key role in determining the fate of the populations.

Evolution of the courter and parenting trait values in each rep with unlinked genetic variation. Dotted line shows the thresholds determining if males become courters (green) or parents (blue)

Evolution of the courter and parenting trait values in each rep with unlinked genetic variation. Dotted line shows the thresholds determining if males become courters (green) or parents (blue)

Without viability selection

This scenario – unlinked loci contributing to the additive genetic variances of courtship and parental traits – is one where having viability selection or not having viability selection is important.

The different runs have different outcomes, but none of the runs crashed. Clearly, the crashing of the populations seen above is due to viability selection.

Let’s look at the morph frequencies for each run.

Frequency of the 4 morphs in each rep with unlinked genetic variation and no viability selection

Frequency of the 4 morphs in each rep with unlinked genetic variation and no viability selection

Frequency of morphs in final generation
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_unlinked_novs_1_summary.txt_1 11999 Pop0 1000 496 504 1000 0.4441960 0.891129 0.7118360 0.505989 1.85068 1.185190 -0.5382970 0.891129 -0.412315 0.238177 1.850680 1.18519 0.1088710 0.000000 0.000000 0.891129 NA NA
parent-courter_unlinked_novs_1_summary.txt_2 11999 Pop1 956 478 478 1000 0.4441960 0.920502 0.7416250 0.501580 1.91364 1.578950 -0.5382970 0.920502 -0.398293 0.236102 1.913640 1.57895 0.0794979 0.000000 0.000000 0.920502 NA NA
parent-courter_unlinked_novs_1_summary.txt_3 11999 Pop2 971 481 490 1000 0.4441960 0.948025 0.7845020 0.506947 1.86184 2.160000 -0.5382970 0.948025 -0.378110 0.238628 1.861840 2.16000 0.0519751 0.000000 0.000000 0.948025 NA NA
parent-courter_unlinked_novs_1_summary.txt_4 11999 Pop3 952 463 489 1000 0.4441960 0.956803 0.7962230 0.507417 1.96614 2.700000 -0.5382970 0.956803 -0.372592 0.238849 1.966140 2.70000 0.0431965 0.000000 0.000000 0.956803 NA NA
parent-courter_unlinked_novs_2_summary.txt_1 11999 Pop0 1000 496 504 1000 0.4441960 0.891129 0.7118360 0.505989 1.85068 1.185190 -0.5382970 0.891129 -0.412315 0.238177 1.850680 1.18519 0.1088710 0.000000 0.000000 0.891129 NA NA
parent-courter_unlinked_novs_2_summary.txt_2 11999 Pop1 956 478 478 1000 0.4441960 0.920502 0.7416250 0.501580 1.91364 1.578950 -0.5382970 0.920502 -0.398293 0.236102 1.913640 1.57895 0.0794979 0.000000 0.000000 0.920502 NA NA
parent-courter_unlinked_novs_2_summary.txt_3 11999 Pop2 971 481 490 1000 0.4441960 0.948025 0.7845020 0.506947 1.86184 2.160000 -0.5382970 0.948025 -0.378110 0.238628 1.861840 2.16000 0.0519751 0.000000 0.000000 0.948025 NA NA
parent-courter_unlinked_novs_2_summary.txt_4 11999 Pop3 952 463 489 1000 0.4441960 0.956803 0.7962230 0.507417 1.96614 2.700000 -0.5382970 0.956803 -0.372592 0.238849 1.966140 2.70000 0.0431965 0.000000 0.000000 0.956803 NA NA
parent-courter_unlinked_novs_3_summary.txt_1 1913 Pop0 6 1 5 4 -0.0598447 0.000000 -0.3739300 0.314086 0.00000 0.000000 0.0997977 1.000000 0.419860 0.320063 0.000000 0.00000 0.0000000 1.000000 0.000000 0.000000 NA NA
parent-courter_unlinked_novs_3_summary.txt_2 1913 Pop1 977 496 481 1000 -0.0598447 0.483871 -0.0831926 0.314898 0.00000 0.398438 0.0997977 0.516129 0.123590 0.320890 0.398438 0.00000 0.0000000 0.516129 0.483871 0.000000 NA NA
parent-courter_unlinked_novs_3_summary.txt_3 1913 Pop2 908 462 446 956 -0.0598447 0.482684 -0.0848639 0.314331 0.00000 0.435146 0.0997977 0.517316 0.125293 0.320313 0.436975 0.00000 0.0000000 0.517316 0.482684 0.000000 NA NA
parent-courter_unlinked_novs_3_summary.txt_4 1913 Pop3 900 464 436 1000 -0.0598447 0.459052 -0.0940052 0.317262 0.00000 0.378486 0.0997977 0.540948 0.134608 0.323300 0.378486 0.00000 0.0000000 0.540948 0.459052 0.000000 NA NA
parent-courter_unlinked_novs_4_summary.txt_1 11999 Pop0 944 456 488 1000 0.0606641 0.951754 0.1924800 0.182530 1.91705 2.909090 0.0498541 0.951754 0.247369 0.273505 1.917050 2.90909 0.0482456 0.000000 0.000000 0.951754 NA NA
parent-courter_unlinked_novs_4_summary.txt_2 11999 Pop1 1000 534 466 1000 0.0606641 0.928839 0.1639050 0.171004 1.64516 1.447370 0.0498541 0.928839 0.204552 0.256235 1.645160 1.44737 0.0711610 0.000000 0.000000 0.928839 NA NA
parent-courter_unlinked_novs_4_summary.txt_3 11999 Pop2 946 469 477 1000 0.0606641 0.901919 0.1456380 0.166740 1.93381 1.652170 0.0498541 0.901919 0.177179 0.249846 1.933810 1.65217 0.0980810 0.000000 0.000000 0.901919 NA NA
parent-courter_unlinked_novs_4_summary.txt_4 11999 Pop3 944 470 474 1000 0.0606641 0.948936 0.1741970 0.172005 1.89686 1.833330 0.0498541 0.948936 0.219973 0.257734 1.896860 1.83333 0.0510638 0.000000 0.000000 0.948936 NA NA
parent-courter_unlinked_novs_5_summary.txt_1 11999 Pop0 952 458 494 1000 -0.4859070 0.938865 -0.0017759 0.502530 2.00465 1.821430 -0.3131550 0.938865 0.331905 0.669575 2.004650 1.82143 0.0611354 0.000000 0.000000 0.938865 NA NA
parent-courter_unlinked_novs_5_summary.txt_2 11999 Pop1 947 469 478 1000 -0.4859070 0.946695 0.0035709 0.503960 1.86712 1.960000 -0.3131550 0.946695 0.339029 0.671480 1.867120 1.96000 0.0533049 0.000000 0.000000 0.946695 NA NA
parent-courter_unlinked_novs_5_summary.txt_3 11999 Pop2 953 487 466 1000 -0.4859070 0.954825 0.0079120 0.506117 1.80000 2.045450 -0.3131550 0.954825 0.344814 0.674354 1.800000 2.04545 0.0451745 0.000000 0.000000 0.954825 NA NA
parent-courter_unlinked_novs_5_summary.txt_4 11999 Pop3 948 448 500 1000 -0.4859070 0.917411 -0.0120651 0.496112 2.00243 1.864860 -0.3131550 0.917411 0.318196 0.661024 2.002430 1.86486 0.0825893 0.000000 0.000000 0.917411 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter.

Evolution of the courter and parenting trait values in each rep with unlinked genetic variation and without viability selection. Green represents courtship trait values and blue represents parental trait values, and the dotted lines are the thresholds

Evolution of the courter and parenting trait values in each rep with unlinked genetic variation and without viability selection. Green represents courtship trait values and blue represents parental trait values, and the dotted lines are the thresholds

When the courter/parent and non-courter/non-parent morphs are maintained in populations, the courter threshold is higher than the parental threshold. When the non-courter/parent and courter/non-parent morphs are maintained, the parental threshold is higher than the courter threshold.

Linked additive genetic variance

In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles anchored on chromosomes, equally distributed among the chromosomes (4). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

With viability selection

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

When only the courtship trait is included in the simulation, 20 of the 20 replicates reached an equilibrium by 10000 generations.

This is further evidenced by looking at a table of trait values and fitnesses in the final generation of each replicate

Frequency of courters with linked QTLs in final generation
CourterFreq CourterW NonCourterW
courter_linked_1_summary.txt_1 1 2.02449 0
courter_linked_1_summary.txt_2 1 1.97217 0
courter_linked_1_summary.txt_3 1 2.12580 0
courter_linked_1_summary.txt_4 1 2.03689 0
courter_linked_2_summary.txt_1 1 2.02449 0
courter_linked_2_summary.txt_2 1 1.97217 0
courter_linked_2_summary.txt_3 1 2.12580 0
courter_linked_2_summary.txt_4 1 2.03689 0
courter_linked_3_summary.txt_1 1 2.15054 0
courter_linked_3_summary.txt_2 1 2.05339 0
courter_linked_3_summary.txt_3 1 2.04499 0
courter_linked_3_summary.txt_4 1 2.04918 0
courter_linked_4_summary.txt_1 1 2.07516 0
courter_linked_4_summary.txt_2 1 2.12876 0
courter_linked_4_summary.txt_3 1 1.97421 0
courter_linked_4_summary.txt_4 1 2.02642 0
courter_linked_5_summary.txt_1 1 2.00401 0
courter_linked_5_summary.txt_2 1 1.94553 0
courter_linked_5_summary.txt_3 1 2.06186 0
courter_linked_5_summary.txt_4 1 2.00803 0

Every replicate has the courtship trait go to fixation.

Let’s also evaluate the evolution of the courtship trait values:

Evolution of courtship trait with linked loci. Green dotted lines are the standard deviations of the traits and the black dotted line is the threshold

Evolution of courtship trait with linked loci. Green dotted lines are the standard deviations of the traits and the black dotted line is the threshold

In every case, the trait values evolve above the threshold.

Without viability selection

Frequency of the courter morph with linked QTLs and no viability selection (each color represents a different replicate)

Frequency of the courter morph with linked QTLs and no viability selection (each color represents a different replicate)

When only the courtship trait is included in the simulation, 0 of the 20 replicates reached an equilibrium by 10000 generations.

This is further evidenced by looking at a table of trait values and fitnesses in the final generation of each replicate

Frequency of courters with linked QTLs in final generation
CourterFreq CourterW NonCourterW
courter_linked_novs_1_summary.txt_1 1 2.05339 0
courter_linked_novs_1_summary.txt_2 1 2.11864 0
courter_linked_novs_1_summary.txt_3 1 1.92308 0
courter_linked_novs_1_summary.txt_4 1 2.02020 0
courter_linked_novs_2_summary.txt_1 1 1.90840 0
courter_linked_novs_2_summary.txt_2 1 1.87617 0
courter_linked_novs_2_summary.txt_3 1 1.98807 0
courter_linked_novs_2_summary.txt_4 1 2.03666 0
courter_linked_novs_3_summary.txt_1 1 2.07469 0
courter_linked_novs_3_summary.txt_2 1 1.99203 0
courter_linked_novs_3_summary.txt_3 1 1.99601 0
courter_linked_novs_3_summary.txt_4 1 1.91571 0
courter_linked_novs_4_summary.txt_1 1 2.04082 0
courter_linked_novs_4_summary.txt_2 1 2.04918 0
courter_linked_novs_4_summary.txt_3 1 2.12314 0
courter_linked_novs_4_summary.txt_4 1 2.01207 0
courter_linked_novs_5_summary.txt_1 1 2.06186 0
courter_linked_novs_5_summary.txt_2 1 1.94553 0
courter_linked_novs_5_summary.txt_3 1 2.08333 0
courter_linked_novs_5_summary.txt_4 1 1.87970 0

Every rep has the courtship trait go to fixation.

Let’s also evaluate the evolution of the courtship trait values:

Evolution of courtship trait with linked loci and without viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of courtship trait with linked loci and without viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

The case with only the courtship trait does not differ qualitatively with or without viability selection.

Parental trait

With viability selection

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parent morph with linked QTLs (each color represents a different replicate)

When only the parental trait is included in the model with linked QTLs, variable outcomes can be reached – although all include each rep reaching some stable state with minor fluctuations.

Frequency of parents with linked QTLs in final generation
ParentFreq ParentW NonParentW
parent_linked_1_summary.txt_1 0.636538 1.36556 0.285714
parent_linked_1_summary.txt_2 0.766798 1.59278 0.406780
parent_linked_1_summary.txt_3 0.694332 1.62099 0.397351
parent_linked_1_summary.txt_4 0.831439 1.59453 0.629213
parent_linked_2_summary.txt_1 0.848303 1.64471 0.539474
parent_linked_2_summary.txt_2 0.761996 1.55919 0.379032
parent_linked_2_summary.txt_3 0.728324 1.51058 0.609929
parent_linked_2_summary.txt_4 0.865759 1.62472 0.695652
parent_linked_3_summary.txt_1 0.873684 1.82169 0.766667
parent_linked_3_summary.txt_2 0.867617 1.69953 0.646154
parent_linked_3_summary.txt_3 0.858586 1.64471 0.714286
parent_linked_3_summary.txt_4 0.861386 1.77471 0.671429
parent_linked_4_summary.txt_1 0.851240 1.70631 0.944444
parent_linked_4_summary.txt_2 0.859155 1.73068 0.657143
parent_linked_4_summary.txt_3 0.872428 1.68868 1.016130
parent_linked_4_summary.txt_4 0.875000 1.64977 0.709677
parent_linked_5_summary.txt_1 0.849237 1.59101 0.607595
parent_linked_5_summary.txt_2 0.690608 1.37600 0.488095
parent_linked_5_summary.txt_3 0.837255 1.52693 0.506024
parent_linked_5_summary.txt_4 0.853465 1.63341 0.608108

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

The evolution of the trait values may shed light on the variable outcomes:

Evolution of parenting trait values with linked QTLs. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with linked QTLs. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Fluctuations around a relatively stable trait mean match the fluctuations around a fairly stable frequency of parental males.

Without viability selection

Frequency of parent morph with linked QTLs without viability selection (each color represents a different replicate)

Frequency of parent morph with linked QTLs without viability selection (each color represents a different replicate)

When only the parental trait is included in the model with linked QTLs, variable outcomes can be reached – although all include each rep reaching some stable state with minor fluctuations.

Frequency of parents with linked QTLs in final generation, with no viability selection
ParentFreq ParentW NonParentW
parent_linked_novs_1_summary.txt_1 0.830116 1.51628 0.420455
parent_linked_novs_1_summary.txt_2 0.794175 1.53545 0.452830
parent_linked_novs_1_summary.txt_3 0.811861 1.72292 0.586957
parent_linked_novs_1_summary.txt_4 0.750973 1.45855 0.468750
parent_linked_novs_2_summary.txt_1 0.838710 1.71635 0.650000
parent_linked_novs_2_summary.txt_2 0.851626 1.69928 0.726027
parent_linked_novs_2_summary.txt_3 0.861660 1.61468 0.571429
parent_linked_novs_2_summary.txt_4 0.892925 1.57602 0.982143
parent_linked_novs_3_summary.txt_1 0.808468 1.70324 0.536842
parent_linked_novs_3_summary.txt_2 0.608696 1.44410 0.410628
parent_linked_novs_3_summary.txt_3 0.669903 1.63188 0.288235
parent_linked_novs_3_summary.txt_4 0.704501 1.53056 0.397351
parent_linked_novs_4_summary.txt_1 0.876310 1.80861 0.932203
parent_linked_novs_4_summary.txt_2 0.599593 1.55932 0.324873
parent_linked_novs_4_summary.txt_3 0.843444 1.51972 0.587500
parent_linked_novs_4_summary.txt_4 0.855397 1.75238 0.619718
parent_linked_novs_5_summary.txt_1 0.730382 1.47934 0.485075
parent_linked_novs_5_summary.txt_2 0.845703 1.62356 0.481013
parent_linked_novs_5_summary.txt_3 0.820866 1.68825 0.472527
parent_linked_novs_5_summary.txt_4 0.834661 1.60143 0.397590

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Looking at the evolution of trait values reflects the same patterns:

Evolution of parenting trait values with linked QTLs and without viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with linked QTLs and without viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Courtship and Parental Traits

Including both courtship and parental traits, along with linked loci, causes the outcomes to be less predictable – same as in the case of unanchored/unlinked genetic loci.

With viability selection

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Because of the variable outcomes, it is useful to visualize the frequencies of the four morphs with each rep in its own graph.

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

In some of the runs the population crashed after few generations. This is obvious both from the figures and when looking at the the final frequencies in a table as well (pay attention to the generation number column):

Frequency of morphs in final generation (linked loci)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_linked_1_summary.txt_1 4433 Pop0 695 362 333 770 -0.1771090 0.4613260 -0.184335 0.0583393 0.000000 0.538462 -0.1405220 0.538674 -0.0907070 0.397158 0.538462 0.000000 0.0000000 0.5386740 0.4613260 0.0000000 NA NA
parent-courter_linked_1_summary.txt_2 4433 Pop1 48 18 30 63 -0.1771090 0.1666670 -0.211818 0.0417545 1.000000 0.466667 -0.1405220 0.888889 0.0802869 0.269718 0.625000 0.000000 0.0000000 0.8333330 0.1111110 0.0555556 NA NA
parent-courter_linked_1_summary.txt_3 4433 Pop2 702 357 345 762 -0.1771090 0.4621850 -0.183445 0.0585249 0.000000 0.526042 -0.1405220 0.535014 -0.0983930 0.398021 0.528796 0.000000 0.0028011 0.5350140 0.4621850 0.0000000 NA NA
parent-courter_linked_1_summary.txt_4 4432 Pop3 6 1 5 4 -0.1771090 0.0000000 -0.223316 0.0462066 0.000000 0.000000 -0.1405220 1.000000 0.1654790 0.306001 0.000000 0.000000 0.0000000 1.0000000 0.0000000 0.0000000 NA NA
parent-courter_linked_2_summary.txt_1 11999 Pop0 1000 534 466 1000 -0.8175180 0.9101120 -0.733446 0.1163110 1.668720 1.229170 -1.0185500 0.900749 -0.8450150 0.242105 1.692310 1.056600 0.0805243 0.0093633 0.0187266 0.8913860 NA NA
parent-courter_linked_2_summary.txt_2 11999 Pop1 999 509 490 1000 -0.8175180 0.9115910 -0.730740 0.1189770 1.859910 1.244440 -1.0185500 0.917485 -0.8370620 0.245982 1.869380 1.095240 0.0707269 0.0176817 0.0117878 0.8998040 NA NA
parent-courter_linked_2_summary.txt_3 11999 Pop2 1000 522 478 1000 -0.8175180 0.8620690 -0.744622 0.1122840 1.760000 0.902778 -1.0185500 0.881226 -0.8528440 0.240554 1.756520 0.790323 0.1091950 0.0287356 0.0095785 0.8524900 NA NA
parent-courter_linked_2_summary.txt_4 11999 Pop3 1000 517 483 1000 -0.8175180 0.8588010 -0.753864 0.0988763 1.704950 0.739726 -1.0185500 0.885880 -0.8873860 0.200243 1.672490 0.762712 0.0947776 0.0464217 0.0193424 0.8394580 NA NA
parent-courter_linked_3_summary.txt_1 11999 Pop0 1000 504 496 1000 0.0263235 0.8869050 0.152153 0.1866310 1.738260 1.087720 0.8752610 0.900794 1.2659500 0.552397 1.744490 0.940000 0.0853175 0.0277778 0.0138889 0.8730160 NA NA
parent-courter_linked_3_summary.txt_2 11999 Pop1 999 502 497 1000 0.0263235 0.8386450 0.134393 0.1803530 1.850360 0.851852 0.8752610 0.854582 1.2108900 0.531859 1.848480 0.753425 0.1235060 0.0378486 0.0219124 0.8167330 NA NA
parent-courter_linked_3_summary.txt_3 11999 Pop2 1000 489 511 1000 0.0263235 0.8711660 0.147093 0.1843960 1.868540 0.984127 0.8752610 0.889571 1.2447300 0.543390 1.848280 1.000000 0.1042940 0.0245399 0.0061350 0.8650310 NA NA
parent-courter_linked_3_summary.txt_4 11999 Pop3 1000 507 493 1000 0.0263235 0.8816570 0.158900 0.1972340 1.798660 1.266670 0.8752610 0.869822 1.2396400 0.544014 1.834470 1.075760 0.1065090 0.0118343 0.0236686 0.8579880 NA NA
parent-courter_linked_4_summary.txt_1 10001 Pop0 825 414 411 920 0.3857320 0.4444440 0.376938 0.0562619 0.000000 0.413043 0.4094560 0.555556 0.4934880 0.537522 0.413043 0.000000 0.0000000 0.5555560 0.4444440 0.0000000 NA NA
parent-courter_linked_4_summary.txt_2 8861 Pop1 4 4 0 0 0.3857320 0.0000000 0.379996 0.0060187 0.000000 0.000000 0.4094560 1.000000 0.5260780 0.120997 0.000000 0.000000 0.0000000 1.0000000 0.0000000 0.0000000 NA NA
parent-courter_linked_4_summary.txt_3 10000 Pop2 52 19 33 72 0.3857320 0.0526316 0.345903 0.0429775 0.000000 0.222222 0.4094560 0.947368 0.7894260 0.410485 0.222222 0.000000 0.0000000 0.9473680 0.0526316 0.0000000 NA NA
parent-courter_linked_4_summary.txt_4 10000 Pop3 866 436 430 952 0.3857320 0.4564220 0.378679 0.0557772 0.040201 0.265823 0.4094560 0.543578 0.4768790 0.533046 0.299578 0.000000 0.0022936 0.5412840 0.4541280 0.0022936 NA NA
parent-courter_linked_5_summary.txt_1 11999 Pop0 1000 510 490 1000 0.4653770 0.8843140 0.596393 0.1915560 1.780490 1.067800 -0.0081426 0.894118 0.3789470 0.555184 1.776320 1.037040 0.0960784 0.0196078 0.0098039 0.8745100 NA NA
parent-courter_linked_5_summary.txt_2 11999 Pop1 958 474 484 1000 0.4653770 0.9556960 0.599532 0.1665730 1.841060 2.523810 -0.0081426 0.953586 0.4044350 0.502434 1.862830 2.045450 0.0358650 0.0084388 0.0105485 0.9451480 NA NA
parent-courter_linked_5_summary.txt_3 11999 Pop2 964 493 471 1000 0.4653770 0.9127790 0.601029 0.1788920 1.793330 0.883721 -0.0081426 0.920892 0.3875940 0.516708 1.795150 0.769231 0.0689655 0.0182556 0.0101420 0.9026370 NA NA
parent-courter_linked_5_summary.txt_4 11999 Pop3 989 503 486 1000 0.4653770 0.9045730 0.594343 0.1860910 1.854950 0.895833 -0.0081426 0.920477 0.3885820 0.553776 1.833690 0.950000 0.0775348 0.0178926 0.0019881 0.9025840 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 5 of those reps with variation actually crashed.

The problems arixe withe courter/non-parent and non-courter/parent morphs start to coexist.

Looking at the trait value evolution may help us understand why some of the runs resulted in extinction:

Evolution of the courter and parenting trait values in each rep with linked genetic variation

Evolution of the courter and parenting trait values in each rep with linked genetic variation

Without viability selection

Same as in the case of unlinked genetic variances, removing viability selection prevents the populations from crashing.

Frequency of the two morphs with linked QTLs and without viability selection (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs and without viability selection (courter = green, parent = blue)

Because of the variable outcomes, it is useful to visualize the frequencies of the four morphs with each rep in its own graph.

Frequency of the 4 morphs in each rep with linked QTLs without viability selection

Frequency of the 4 morphs in each rep with linked QTLs without viability selection

In some of the runs the population crashed after few generations. This is obvious both from the figures and when looking at the the final frequencies in a table as well (pay attention to the generation number column):

Frequency of morphs in final generation (linked loci, no viability selection)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_linked_novs_1_summary.txt_1 11999 Pop0 1000 480 520 1000 0.933615 0.897917 1.333910 0.579584 1.9373500 1.306120 -0.114728 0.893750 0.182179 0.4312150 1.967370 1.078430 0.0895833 0.0125000 0.0166667 0.8812500 NA NA
parent-courter_linked_novs_1_summary.txt_2 11999 Pop1 993 499 494 1000 0.933615 0.885772 1.314860 0.563536 1.8936700 1.140350 -0.114728 0.887776 0.160480 0.4118220 1.896160 1.107140 0.1042080 0.0100200 0.0080160 0.8777560 NA NA
parent-courter_linked_novs_1_summary.txt_3 11999 Pop2 989 461 528 1000 0.933615 0.893709 1.335020 0.576297 2.0048500 1.367350 -0.114728 0.908894 0.191017 0.4312860 1.983290 1.476190 0.0867679 0.0195228 0.0043384 0.8893710 NA NA
parent-courter_linked_novs_1_summary.txt_4 11999 Pop3 993 513 480 1000 0.933615 0.851852 1.265330 0.522345 1.7597300 1.092110 -0.114728 0.867446 0.137293 0.3860480 1.759550 1.014710 0.1130600 0.0350877 0.0194932 0.8323590 NA NA
parent-courter_linked_novs_2_summary.txt_1 11999 Pop0 1000 493 507 1000 0.933615 0.920892 1.397390 0.621610 1.8281900 1.282050 -0.114728 0.920892 0.218400 0.4506270 1.848020 1.051280 0.0669371 0.0121704 0.0121704 0.9087220 NA NA
parent-courter_linked_novs_2_summary.txt_2 11999 Pop1 1000 526 474 1000 0.933615 0.910646 1.342900 0.567567 1.7411300 1.191490 -0.114728 0.927757 0.215363 0.4381490 1.739750 1.078950 0.0665399 0.0228137 0.0057034 0.9049430 NA NA
parent-courter_linked_novs_2_summary.txt_3 11999 Pop2 1000 506 494 1000 0.933615 0.899209 1.353970 0.582419 1.7868100 0.686275 -0.114728 0.909091 0.189434 0.4227330 1.776090 0.673913 0.0849802 0.0158103 0.0059288 0.8932810 NA NA
parent-courter_linked_novs_2_summary.txt_4 11999 Pop3 1000 467 533 1000 0.933615 0.877944 1.347710 0.617913 1.9902400 1.333330 -0.114728 0.890792 0.179219 0.4437650 1.978370 1.352940 0.1049250 0.0171306 0.0042827 0.8736620 NA NA
parent-courter_linked_novs_3_summary.txt_1 11999 Pop0 1000 493 507 1000 0.933615 0.920892 1.397390 0.621610 1.8281900 1.282050 -0.114728 0.920892 0.218400 0.4506270 1.848020 1.051280 0.0669371 0.0121704 0.0121704 0.9087220 NA NA
parent-courter_linked_novs_3_summary.txt_2 11999 Pop1 1000 526 474 1000 0.933615 0.910646 1.342900 0.567567 1.7411300 1.191490 -0.114728 0.927757 0.215363 0.4381490 1.739750 1.078950 0.0665399 0.0228137 0.0057034 0.9049430 NA NA
parent-courter_linked_novs_3_summary.txt_3 11999 Pop2 1000 506 494 1000 0.933615 0.899209 1.353970 0.582419 1.7868100 0.686275 -0.114728 0.909091 0.189434 0.4227330 1.776090 0.673913 0.0849802 0.0158103 0.0059288 0.8932810 NA NA
parent-courter_linked_novs_3_summary.txt_4 11999 Pop3 1000 467 533 1000 0.933615 0.877944 1.347710 0.617913 1.9902400 1.333330 -0.114728 0.890792 0.179219 0.4437650 1.978370 1.352940 0.1049250 0.0171306 0.0042827 0.8736620 NA NA
parent-courter_linked_novs_4_summary.txt_1 11999 Pop0 980 512 468 1000 -0.105665 0.464844 -0.114794 0.108740 0.0294118 0.412409 -0.359170 0.537109 -0.356093 0.0364008 0.436364 0.000000 0.0019531 0.5332030 0.4609380 0.0039062 NA NA
parent-courter_linked_novs_4_summary.txt_2 11999 Pop1 980 499 481 1000 -0.105665 0.464930 -0.112029 0.107393 0.0000000 0.453184 -0.359170 0.535070 -0.356999 0.0359518 0.453184 0.000000 0.0000000 0.5350700 0.4649300 0.0000000 NA NA
parent-courter_linked_novs_4_summary.txt_3 11999 Pop2 979 504 475 1000 -0.105665 0.462302 -0.114977 0.109187 0.0000000 0.372694 -0.359170 0.535714 -0.356055 0.0365506 0.374074 0.000000 0.0019841 0.5357140 0.4623020 0.0000000 NA NA
parent-courter_linked_novs_4_summary.txt_4 11999 Pop3 983 515 468 1000 -0.105665 0.454369 -0.116693 0.108979 0.0000000 0.327402 -0.359170 0.545631 -0.355486 0.0364892 0.327402 0.000000 0.0000000 0.5456310 0.4543690 0.0000000 NA NA
parent-courter_linked_novs_5_summary.txt_1 11999 Pop0 980 512 468 1000 -0.105665 0.464844 -0.114794 0.108740 0.0294118 0.412409 -0.359170 0.537109 -0.356093 0.0364008 0.436364 0.000000 0.0019531 0.5332030 0.4609380 0.0039062 NA NA
parent-courter_linked_novs_5_summary.txt_2 11999 Pop1 980 499 481 1000 -0.105665 0.464930 -0.112029 0.107393 0.0000000 0.453184 -0.359170 0.535070 -0.356999 0.0359518 0.453184 0.000000 0.0000000 0.5350700 0.4649300 0.0000000 NA NA
parent-courter_linked_novs_5_summary.txt_3 11999 Pop2 979 504 475 1000 -0.105665 0.462302 -0.114977 0.109187 0.0000000 0.372694 -0.359170 0.535714 -0.356055 0.0365506 0.374074 0.000000 0.0019841 0.5357140 0.4623020 0.0000000 NA NA
parent-courter_linked_novs_5_summary.txt_4 11999 Pop3 983 515 468 1000 -0.105665 0.454369 -0.116693 0.108979 0.0000000 0.327402 -0.359170 0.545631 -0.355486 0.0364892 0.327402 0.000000 0.0000000 0.5456310 0.4543690 0.0000000 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs have two morphs coexisting.

Looking at the trait value evolution may help us understand why some of the runs resulted in extinction:

Evolution of the courter and parenting trait values in each rep with linked genetic variation and no viability selection

Evolution of the courter and parenting trait values in each rep with linked genetic variation and no viability selection

Same as with unlinked variation, when the parental threshold is higher than the courtship threshold, the non-courter/parent and parent/non-courter coexist.

Supergenes

In these cases, the loci (50) are all located in one region of a chromosome, and that region has reduced recombination. As above, the overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

With viability selection

Frequency of the courter morph with supergenes (each color represents a different replicate)

Frequency of the courter morph with supergenes (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with supergenes in final generation
CourterFreq CourterW NonCourterW
courter_supergene_1_summary.txt_1 1 1.94129 0
courter_supergene_1_summary.txt_2 1 2.04107 0
courter_supergene_1_summary.txt_3 1 1.95098 0
courter_supergene_1_summary.txt_4 1 2.04733 0
courter_supergene_2_summary.txt_1 1 1.98603 0
courter_supergene_2_summary.txt_2 1 2.05144 0
courter_supergene_2_summary.txt_3 1 1.97624 0
courter_supergene_2_summary.txt_4 1 1.98403 0
courter_supergene_3_summary.txt_1 1 2.02429 0
courter_supergene_3_summary.txt_2 1 2.04959 0
courter_supergene_3_summary.txt_3 1 1.94727 0
courter_supergene_3_summary.txt_4 1 1.93217 0
courter_supergene_4_summary.txt_1 1 1.96850 0
courter_supergene_4_summary.txt_2 1 1.96078 0
courter_supergene_4_summary.txt_3 1 1.96850 0
courter_supergene_4_summary.txt_4 1 1.76056 0
courter_supergene_5_summary.txt_1 1 1.80435 0
courter_supergene_5_summary.txt_2 1 1.97809 0
courter_supergene_5_summary.txt_3 1 1.99399 0
courter_supergene_5_summary.txt_4 1 1.94706 0

Looking at the evolution of the trait values:

Evolution of courtship trait with a supergene. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of courtship trait with a supergene. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Without viability selection

Frequency of the courter morph with supergenes without viability selection (each color represents a different replicate)

Frequency of the courter morph with supergenes without viability selection (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with supergenes in final generation with no viability selection
CourterFreq CourterW NonCourterW
courter_supergene_novs_1_summary.txt_1 1 2.06186 0
courter_supergene_novs_1_summary.txt_2 1 1.98020 0
courter_supergene_novs_1_summary.txt_3 1 1.94553 0
courter_supergene_novs_1_summary.txt_4 1 1.96464 0
courter_supergene_novs_2_summary.txt_1 1 1.91571 0
courter_supergene_novs_2_summary.txt_2 1 2.01613 0
courter_supergene_novs_2_summary.txt_3 1 2.03252 0
courter_supergene_novs_2_summary.txt_4 1 1.99203 0
courter_supergene_novs_3_summary.txt_1 1 1.93424 0
courter_supergene_novs_3_summary.txt_2 1 2.00803 0
courter_supergene_novs_3_summary.txt_3 1 1.96464 0
courter_supergene_novs_3_summary.txt_4 1 1.98807 0
courter_supergene_novs_4_summary.txt_1 1 1.93424 0
courter_supergene_novs_4_summary.txt_2 1 2.00803 0
courter_supergene_novs_4_summary.txt_3 1 1.96464 0
courter_supergene_novs_4_summary.txt_4 1 1.98807 0
courter_supergene_novs_5_summary.txt_1 1 1.89753 0
courter_supergene_novs_5_summary.txt_2 1 1.93424 0
courter_supergene_novs_5_summary.txt_3 1 1.98807 0
courter_supergene_novs_5_summary.txt_4 1 2.08768 0

Looking at the evolution of the trait values:

Evolution of courtship trait with a supergene and without viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of courtship trait with a supergene and without viability selection. Green dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Parental trait

With viability selection

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parents with supergenes in final generation
ParentFreq ParentW NonParentW
parent_supergene_1_summary.txt_1 0.859244 1.77262 0.791045
parent_supergene_1_summary.txt_2 0.873727 1.66667 0.596774
parent_supergene_1_summary.txt_3 0.851852 1.63285 0.805556
parent_supergene_1_summary.txt_4 0.873823 1.52802 0.776119
parent_supergene_2_summary.txt_1 0.517034 1.45349 0.261411
parent_supergene_2_summary.txt_2 0.557769 1.54643 0.252252
parent_supergene_2_summary.txt_3 0.463265 1.36564 0.418251
parent_supergene_2_summary.txt_4 0.514344 1.47809 0.219409
parent_supergene_3_summary.txt_1 0.866534 1.60230 0.761194
parent_supergene_3_summary.txt_2 0.880157 1.65179 0.786885
parent_supergene_3_summary.txt_3 0.875248 1.67873 0.730159
parent_supergene_3_summary.txt_4 0.869121 1.74118 0.828125
parent_supergene_4_summary.txt_1 0.520085 1.47561 0.378855
parent_supergene_4_summary.txt_2 0.487179 1.37247 0.269231
parent_supergene_4_summary.txt_3 0.502174 1.70130 0.423581
parent_supergene_4_summary.txt_4 0.525105 1.65600 0.219298
parent_supergene_5_summary.txt_1 0.539370 1.39781 0.358974
parent_supergene_5_summary.txt_2 0.520000 1.34066 0.214286
parent_supergene_5_summary.txt_3 0.518519 1.43214 0.284615
parent_supergene_5_summary.txt_4 0.542074 1.56679 0.320513

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Let’s look at the trajectories of the parent traits.

Evolution of parenting trait values with a supergene. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with a supergene. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Without viability selection

Frequency of parent morph with supergenes without viability selection (each color represents a different replicate)

Frequency of parent morph with supergenes without viability selection (each color represents a different replicate)

Frequency of parents with supergenes in final generation without viability selection
ParentFreq ParentW NonParentW
parent_supergene_novs_1_summary.txt_1 0.833656 1.62413 0.488372
parent_supergene_novs_1_summary.txt_2 0.868110 1.63492 0.656716
parent_supergene_novs_1_summary.txt_3 0.878193 1.68456 1.048390
parent_supergene_novs_1_summary.txt_4 0.844758 1.61814 0.727273
parent_supergene_novs_2_summary.txt_1 0.557613 1.40959 0.376744
parent_supergene_novs_2_summary.txt_2 0.488978 1.47951 0.247059
parent_supergene_novs_2_summary.txt_3 0.479424 1.36910 0.296443
parent_supergene_novs_2_summary.txt_4 0.508299 1.44082 0.312236
parent_supergene_novs_3_summary.txt_1 0.907514 1.58174 0.895833
parent_supergene_novs_3_summary.txt_2 0.885593 1.77990 0.870370
parent_supergene_novs_3_summary.txt_3 0.907869 1.61099 1.083330
parent_supergene_novs_3_summary.txt_4 0.876797 1.69321 0.750000
parent_supergene_novs_4_summary.txt_1 0.907514 1.58174 0.895833
parent_supergene_novs_4_summary.txt_2 0.885593 1.77990 0.870370
parent_supergene_novs_4_summary.txt_3 0.907869 1.61099 1.083330
parent_supergene_novs_4_summary.txt_4 0.876797 1.69321 0.750000
parent_supergene_novs_5_summary.txt_1 0.580517 1.43836 0.289100
parent_supergene_novs_5_summary.txt_2 0.534483 1.49462 0.246914
parent_supergene_novs_5_summary.txt_3 0.541825 1.50175 0.215768
parent_supergene_novs_5_summary.txt_4 0.533865 1.45522 0.252137

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Let’s look at the trajectories of the parent traits.

Evolution of parenting trait values with a supergene without viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Evolution of parenting trait values with a supergene without viability selection. Blue dotted lines are the standard deviations around the mean and the black dotted line is the threshold

Courtship and Parental Traits

With viability selection

The different runs have different outcomes. To better see this, let’s look at the morph frequencies in each rep separately.

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

Frequency of morphs in final generation (supergenes)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_supergene_1_summary.txt_1 825 Pop0 271 137 134 289 0.2014990 0.467153 0.1787730 0.0680367 0.00000 0.452055 0.933871 0.532847 0.9769160 0.128869 0.452055 0.00000 0.0000000 0.532847 0.4671530 0.000000 NA NA
parent-courter_supergene_1_summary.txt_2 240 Pop1 4 4 0 0 0.2014990 0.000000 0.1241530 0.0773462 0.00000 0.000000 0.933871 1.000000 1.0803700 0.146502 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_1_summary.txt_3 205 Pop2 4 4 0 0 0.2014990 0.000000 0.1241530 0.0773462 0.00000 0.000000 0.933871 1.000000 1.0803700 0.146502 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_1_summary.txt_4 824 Pop3 6 6 0 0 0.2014990 0.000000 0.1241530 0.0773462 0.00000 0.000000 0.933871 1.000000 1.0803700 0.146502 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_2_summary.txt_1 235 Pop0 7 1 6 4 -0.6500140 0.000000 -1.4793200 0.8293020 0.00000 0.000000 -0.511526 1.000000 0.1149370 0.626463 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_2_summary.txt_2 192 Pop1 4 4 0 0 -0.6500140 0.500000 -1.0495400 0.5867950 0.00000 0.000000 -0.511526 0.500000 -0.2097210 0.443271 0.000000 0.00000 0.0000000 0.500000 0.5000000 0.000000 NA NA
parent-courter_supergene_2_summary.txt_3 168 Pop2 4 4 0 0 -0.6500140 0.000000 -1.4793200 0.8293020 0.00000 0.000000 -0.511526 1.000000 0.1149370 0.626463 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_2_summary.txt_4 235 Pop3 31 13 18 40 -0.6500140 0.230769 -1.2809600 0.7274910 0.00000 0.300000 -0.511526 0.769231 -0.0349049 0.549554 0.300000 0.00000 0.0000000 0.769231 0.2307690 0.000000 NA NA
parent-courter_supergene_3_summary.txt_1 11999 Pop0 948 489 459 1000 -0.0371052 0.648262 -0.0373701 0.0218645 1.34385 0.389535 -0.502682 0.777096 -0.3643700 0.211891 1.297370 0.00000 0.0000000 0.351738 0.2229040 0.425358 NA NA
parent-courter_supergene_3_summary.txt_2 11999 Pop1 945 470 475 1000 -0.0371052 0.808511 -0.0289095 0.0224271 1.71053 0.855556 -0.502682 0.946809 -0.2210240 0.334887 1.633710 0.00000 0.0000000 0.191489 0.0531915 0.755319 NA NA
parent-courter_supergene_3_summary.txt_3 11999 Pop2 939 490 449 1000 -0.0371052 0.834694 -0.0279147 0.0222429 1.64059 0.617284 -0.502682 0.959184 -0.1935640 0.358014 1.534040 0.00000 0.0000000 0.165306 0.0408163 0.793878 NA NA
parent-courter_supergene_3_summary.txt_4 11999 Pop3 944 450 494 1000 -0.0371052 0.875556 -0.0229953 0.0247926 1.81218 0.642857 -0.502682 0.951111 -0.1798290 0.368457 1.752340 0.00000 0.0000000 0.124444 0.0488889 0.826667 NA NA
parent-courter_supergene_4_summary.txt_1 11999 Pop0 948 489 459 1000 -0.0371052 0.648262 -0.0373701 0.0218645 1.34385 0.389535 -0.502682 0.777096 -0.3643700 0.211891 1.297370 0.00000 0.0000000 0.351738 0.2229040 0.425358 NA NA
parent-courter_supergene_4_summary.txt_2 11999 Pop1 945 470 475 1000 -0.0371052 0.808511 -0.0289095 0.0224271 1.71053 0.855556 -0.502682 0.946809 -0.2210240 0.334887 1.633710 0.00000 0.0000000 0.191489 0.0531915 0.755319 NA NA
parent-courter_supergene_4_summary.txt_3 11999 Pop2 939 490 449 1000 -0.0371052 0.834694 -0.0279147 0.0222429 1.64059 0.617284 -0.502682 0.959184 -0.1935640 0.358014 1.534040 0.00000 0.0000000 0.165306 0.0408163 0.793878 NA NA
parent-courter_supergene_4_summary.txt_4 11999 Pop3 944 450 494 1000 -0.0371052 0.875556 -0.0229953 0.0247926 1.81218 0.642857 -0.502682 0.951111 -0.1798290 0.368457 1.752340 0.00000 0.0000000 0.124444 0.0488889 0.826667 NA NA
parent-courter_supergene_5_summary.txt_1 11999 Pop0 943 450 493 1000 -0.4859070 0.935556 -0.0035635 0.5016590 1.94537 1.724140 -0.313155 0.935556 0.3295240 0.668414 1.945370 1.72414 0.0644444 0.000000 0.0000000 0.935556 NA NA
parent-courter_supergene_5_summary.txt_2 11999 Pop1 935 460 475 1000 -0.4859070 0.904348 -0.0213614 0.4939030 2.02644 1.318180 -0.313155 0.904348 0.3058090 0.658080 2.026440 1.31818 0.0956522 0.000000 0.0000000 0.904348 NA NA
parent-courter_supergene_5_summary.txt_3 11999 Pop2 944 469 475 1000 -0.4859070 0.927505 -0.0078137 0.4994760 1.92184 1.852940 -0.313155 0.927505 0.3238610 0.665507 1.921840 1.85294 0.0724947 0.000000 0.0000000 0.927505 NA NA
parent-courter_supergene_5_summary.txt_4 11999 Pop3 944 470 474 1000 -0.4859070 0.923404 -0.0088650 0.4977280 1.91475 1.527780 -0.313155 0.923404 0.3224600 0.663177 1.914750 1.52778 0.0765957 0.000000 0.0000000 0.923404 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. 8 of those reps with variation went extinct before 10000 generations.

Evolution of the courter and parenting trait values in each rep with a supergene

Evolution of the courter and parenting trait values in each rep with a supergene

Without viability selection

The different runs have different outcomes. To better see this, let’s look at the morph frequencies in each rep separately.

Frequency of the 4 morphs in each rep with supergenes without viability selection

Frequency of the 4 morphs in each rep with supergenes without viability selection

Frequency of morphs in final generation (supergenes and no viability selection)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentAEmean ParentAEsd ParentW NonParentW CourterThresh CourterFreq CourterAEmean CourterAEsd CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_supergene_novs_1_summary.txt_1 236 Pop0 663 340 323 724 0.2014990 0.467647 0.1897210 0.0740912 0.00000 0.287293 0.933871 0.532353 0.956180 0.140337 0.287293 0.00000 0.0000000 0.532353 0.4676470 0.000000 NA NA
parent-courter_supergene_novs_1_summary.txt_2 235 Pop1 8 1 7 4 0.2014990 0.000000 0.1241530 0.0773462 0.00000 0.000000 0.933871 1.000000 1.080370 0.146502 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_novs_1_summary.txt_3 235 Pop2 12 7 5 16 0.2014990 0.000000 0.1241530 0.0773462 0.00000 0.000000 0.933871 1.000000 1.080370 0.146502 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_novs_1_summary.txt_4 235 Pop3 35 17 18 47 0.2014990 0.294118 0.1470790 0.0649846 0.00000 0.500000 0.933871 0.705882 1.036950 0.123088 0.500000 0.00000 0.0000000 0.705882 0.2941180 0.000000 NA NA
parent-courter_supergene_novs_2_summary.txt_1 11999 Pop0 957 465 492 1000 1.1680300 0.920430 1.9078000 0.7783020 1.98598 1.675680 0.474500 0.920430 1.166300 0.727828 1.985980 1.67568 0.0795699 0.000000 0.0000000 0.920430 NA NA
parent-courter_supergene_novs_2_summary.txt_2 11999 Pop1 950 491 459 1000 1.1680300 0.920570 1.9062700 0.7793740 1.80531 1.820510 0.474500 0.920570 1.164870 0.728830 1.805310 1.82051 0.0794297 0.000000 0.0000000 0.920570 NA NA
parent-courter_supergene_novs_2_summary.txt_3 11999 Pop2 956 487 469 1000 1.1680300 0.913758 1.9039200 0.7743560 1.86966 1.500000 0.474500 0.913758 1.162670 0.724138 1.869660 1.50000 0.0862423 0.000000 0.0000000 0.913758 NA NA
parent-courter_supergene_novs_2_summary.txt_4 11999 Pop3 956 489 467 1000 1.1680300 0.924335 1.9094900 0.7809600 1.87832 1.486490 0.474500 0.924335 1.167880 0.730313 1.878320 1.48649 0.0756646 0.000000 0.0000000 0.924335 NA NA
parent-courter_supergene_novs_3_summary.txt_1 396 Pop0 12 1 11 4 0.3857320 0.000000 0.3267080 0.0590242 0.00000 0.000000 0.409456 1.000000 0.973460 0.564004 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_novs_3_summary.txt_2 396 Pop1 67 30 37 84 0.3857320 0.300000 0.3444500 0.0493832 0.00000 0.523810 0.409456 0.700000 0.803926 0.471880 0.523810 0.00000 0.0000000 0.700000 0.3000000 0.000000 NA NA
parent-courter_supergene_novs_3_summary.txt_3 396 Pop2 16 5 11 20 0.3857320 0.000000 0.3267080 0.0590242 0.00000 0.000000 0.409456 1.000000 0.973460 0.564004 0.000000 0.00000 0.0000000 1.000000 0.0000000 0.000000 NA NA
parent-courter_supergene_novs_3_summary.txt_4 396 Pop3 80 34 46 103 0.3857320 0.235294 0.3406240 0.0516152 0.00000 0.692308 0.409456 0.764706 0.840492 0.493208 0.692308 0.00000 0.0000000 0.764706 0.2352940 0.000000 NA NA
parent-courter_supergene_novs_4_summary.txt_1 11999 Pop0 948 470 478 1000 -0.0371052 0.791489 -0.0264495 0.0253636 1.69624 0.479592 -0.502682 0.910638 -0.231110 0.334517 1.584110 0.00000 0.0000000 0.208511 0.0893617 0.702128 NA NA
parent-courter_supergene_novs_4_summary.txt_2 11999 Pop1 948 458 490 1000 -0.0371052 0.810044 -0.0268243 0.0242702 1.67116 0.540230 -0.502682 0.934498 -0.216340 0.342636 1.558410 0.00000 0.0000000 0.189956 0.0655022 0.744541 NA NA
parent-courter_supergene_novs_4_summary.txt_3 11999 Pop2 946 481 465 1000 -0.0371052 0.891892 -0.0227781 0.0239164 1.73893 0.807692 -0.502682 0.954262 -0.161070 0.384389 1.716780 0.00000 0.0000000 0.108108 0.0457380 0.846154 NA NA
parent-courter_supergene_novs_4_summary.txt_4 11999 Pop3 943 477 466 1000 -0.0371052 0.863732 -0.0265996 0.0218090 1.68447 0.707692 -0.502682 0.955975 -0.177442 0.371442 1.622810 0.00000 0.0000000 0.136268 0.0440252 0.819706 NA NA
parent-courter_supergene_novs_5_summary.txt_1 11999 Pop0 943 493 450 1000 -0.4859070 0.918864 -0.0134552 0.4977370 1.85872 1.400000 -0.313155 0.918864 0.316344 0.663189 1.858720 1.40000 0.0811359 0.000000 0.0000000 0.918864 NA NA
parent-courter_supergene_novs_5_summary.txt_2 11999 Pop1 949 478 471 1000 -0.4859070 0.949791 0.0052238 0.5047820 1.89427 1.958330 -0.313155 0.949791 0.341232 0.672576 1.894270 1.95833 0.0502092 0.000000 0.0000000 0.949791 NA NA
parent-courter_supergene_novs_5_summary.txt_3 11999 Pop2 956 480 476 1000 -0.4859070 0.912500 -0.0157995 0.4954190 1.89041 1.500000 -0.313155 0.912500 0.313220 0.660101 1.890410 1.50000 0.0875000 0.000000 0.0000000 0.912500 NA NA
parent-courter_supergene_novs_5_summary.txt_4 11999 Pop3 944 470 474 1000 -0.4859070 0.940426 0.0002233 0.5022900 1.83710 2.214290 -0.313155 0.940426 0.334569 0.669255 1.837100 2.21429 0.0595745 0.000000 0.0000000 0.940426 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. 8 of those reps with variation went extinct before 10000 generations.

Evolution of the courter and parenting trait values in each rep with a supergene without viability selection

Evolution of the courter and parenting trait values in each rep with a supergene without viability selection

In the case of supergenes, the qualitative outcomes differ substantially between the viability and no-viability runs, but not in terms of populations crashing or surviving – different types of variation can be maintained!

Preliminary conclusions